Although I have never really tried to "Disable" the whole storyline, but in theory this should work, if it doesn't, then you might try the file "Game\CustomInit.xml" and see if you can Change the FirstMissionName to an Empty Mission.

you can avoid the story line without much scripting.
1. just select and modify favourite mothership as you like - in config files
2. add good equipment, pilots, etc. - script
3. start game - follow story until you come to station in second sector, where unhappy boy want deliver cargo to scientific station and decline task.
3. you can flee free as bird to all sectors, with exception, where is it "disabled" by story (example - mines field)
4. you can return to story as you like, ship will be exchanged as usualy, equipment will be stored to cargo space.